Mercurial > repos > aaronquinlan > multi_intersect

comparison BEDTools-Version-2.14.3/src/annotateBed/annotateBed.h @ 0:dfcd8b6c1bda

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author aaronquinlan
date Thu, 03 Nov 2011 10:25:04 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:dfcd8b6c1bda
1 /*****************************************************************************
2 annotateBed.h
3
4 (c) 2009 - Aaron Quinlan
5 Hall Laboratory
6 Department of Biochemistry and Molecular Genetics
7 University of Virginia
8 aaronquinlan@gmail.com
9
10 Licenced under the GNU General Public License 2.0 license.
11 ******************************************************************************/
12 #ifndef ANNOTATEBED_H
13 #define ANNOTATEBED_H
14
15 #include "bedFile.h"
16 #include <vector>
17 #include <algorithm>
18 #include <iostream>
19 #include <iomanip>
20 #include <fstream>
21 #include <stdlib.h>
22
23 using namespace std;
24
25 //************************************************
26 // Class methods and elements
27 //************************************************
28 class BedAnnotate {
29
30 public:
31
32 // constructor
33 BedAnnotate(const string &mainFile, const vector<string> &annoFileNames,
34 const vector<string> &annoTitles, bool sameStrand, bool diffStrand, bool reportCounts, bool reportBoth);
35
36 // destructor
37 ~BedAnnotate(void);
38
39 // annotate the master file with all of the annotation files.
40 void AnnotateBed();
41
42 private:
43
44 // input files.
45 string _mainFile;
46 vector<string> _annoFileNames;
47 vector<string> _annoTitles;
48
49 // instance of a bed file class.
50 BedFile *_bed;
51 vector<BedFile*> _annoFiles;
52
53 // do we care about strandedness when counting coverage?
54 bool _sameStrand;
55 bool _diffStrand;
56
57 bool _reportCounts;
58 bool _reportBoth;
59
60 // private function for reporting coverage information
61 void ReportAnnotations();
62
63 void OpenAnnoFiles();
64
65 void CloseAnnoFiles();
66
67 void PrintHeader();
68
69 void InitializeMainFile();
70 };
71 #endif /* ANNOTATEBED_H */